This has nothing to do with causality.
The fact remains that induction is fundamentally flawed in both theory and practice. If you observe something, observing it only tells you that it holds for that case (and that the negative cannot hold for every case). Again, the example of the black swan is wonderfully illustrative of this fact, everyone "knew" all swans were white, until a black swan was found.
Thus, we have have the problem of induction, something modern science deftly sidestepped by going for infinite tests (the only way to make induction rigorous). In practice, this means that nothing is ever proven 100%, there's always a chance a new observation will disprove something that you've believed for your entire life. It happened with the movement of tectonic plates (in HS they believed it was convection currents that caused it, so I was taught that, a few years they discovered it was gravity, so in geology class I was taught that), and it can happen with anything else.
Science cannot prove that historical evolution is what happened as it stands, in fact it's constantly being disproven, replaced with explanations that better fit new evidence. However it can prove that the process of evolution occurs (since it has been observed).
While this issue may be covered in philosophy, it's fundamentally a practical one, induction is bad, but it's all we have to base science upon.